The present invention relates to the field of sample processing devices and methods. More particularly, the present invention relates to sample processing devices with integral electrophoresis channels and methods of loading the electrophoresis channels with an electrophoresis sieving polymer.
The preparation of a biological sample for, e.g., DNA sequencing and detection can involve a number of critical processes and transfers. For example, a user may be required to prepare a biological sample input (e.g., purified DNA target, whole blood/tissue, etc.) and extraction/clean-up. After these steps are completed, the sample materials may typically undergo polymerase chain reaction (PCR) amplification, clean-up and possible detection. The prepared PCR amplification products may then undergo Sanger amplification and clean-up. Following these steps, the end product of the processed sample material may undergo electrophoresis and fluorescence detection.
Each of these procedures can require considerable human intervention and a number of fluid transfers, all of which can result in errors, contamination, and exposure to potential biohazards. Furthermore, the time required from sample input to sequence data output can, in some instances be up to 24 hours or more. In addition, the various equipment required to perform the different procedures may cost, e.g., US$100,000 to about US$200,000 or more, thereby increasing the cost of the processing. Further, the personnel performing these procedures are typically highly-skilled, with expertise in DNA sample preparation, machine interface/maintenance, analysis and quality control.
Furthermore, it is important that electrophoresis sieving polymer located along an electrophoresis path, e.g., a capillary or slab, be substantially, if not completely, free of voids and/or bubbles to allow for accurate separation of the analyte. Many different techniques have been developed for loading electrophoresis sieving polymer into capillaries and other electrophoresis devices. Many of these techniques, however, do not allow for the removal of voids and/or bubbles after they are located within the electrophoresis sieving polymer, requiring complete removal of the electrophoresis sieving polymer and reloading or simply discarding the device and beginning with a new device.
The present invention provides a sample processing device with electrophoresis channels and methods of loading the electrophoresis channels with electrophoresis sieving polymer while rotating the sample processing device.
The sample processing devices are designed for processing sample materials that include chemical and/or biological mixtures. If the sample materials include a biological mixture, the biological mixture preferably includes biological material such as peptide- and/or nucleotide-containing material. It may further be preferred that the biological mixture include a nucleic acid amplification reaction mixture (e.g., a PCR reaction mixture or a nucleic acid sequencing reaction mixture).
In some instances, the electrophoresis channels may be arranged radially relative to the axis of rotation of the sample processing device. In other sample processing devices, the electrophoresis channels may be arranged in curved arcs that are concentric about the center of the sample processing device (which preferably corresponds to the axis of rotation).
Further, the electrophoresis channels may in some instances be unvented, such that the only opening into or out of the electrophoresis channel is located proximate the chamber or port into which the electrophoresis sieving polymer or other sample materials are introduced. In an unvented electrophoresis channel, the terminal end of the electrophoresis channel, i.e., the end distal from the axis of rotation and/or the loading chamber, is sealed to prevent the exit of fluids from the electrophoresis channel.
Sample processing devices in which the electrophoresis channels are vented proximate their terminal ends may preferably include a flow restrictor along the path followed by the electrophoresis sieving polymer during loading of the electrophoresis channel. The flow restrictor may be, e.g., a closed valve that prevents fluid flow until opened, or it may be in the form of a constricted passage through which the electrophoresis sieving polymer must travel during loading.
Regardless of whether the sample processing devices include a valve or a constricted passage, rotation of the sample processing device with the electrophoresis sieving polymer located therein for delivery to the electrophoresis channels provides a significant advantage in that the fluid pressure generated in the electrophoresis sieving polymer during rotation before the electrophoresis sieving polymer passes through the flow restrictor (e.g., while the valve is closed) substantially, if not completely, removes any bubbles sufficiently large to adversely affect the separation to be performed in the electrophoresis channel.
Another advantage of sample processing devices according to the present invention is that even if bubbles or voids are located in the electrophoresis channels after loading with electrophoresis sieving polymer, the bubbles or voids may be removed by further rotation of the sample processing device. In other words, what could be considered a failure during loading can be corrected by additional rotation of the sample processing device (in contrast to the known methods and devices in which the electrophoresis channel must be emptied and reloaded or simply discarded).
In one aspect, the present invention includes a method of providing an electrophoresis channel containing an electrophoresis sieving polymer by providing a device having a plurality of electrophoresis channels and at least one electrophoresis medium chamber; providing electrophoresis sieving polymer in the at least one electrophoresis medium chamber; and rotating the device about an axis of rotation while the at least one electrophoresis medium chamber is in fluid communication with each electrophoresis channel of the plurality of electrophoresis channels, wherein the at least one electrophoresis medium chamber is located radially inward from the plurality of electrophoresis channels relative to the axis of rotation. During rotation of the device, the electrophoresis sieving polymer in the at least one electrophoresis medium chamber moves into the plurality of electrophoresis channels.
In another aspect, the present invention includes a method of providing an electrophoresis channel containing an electrophoresis sieving polymer by providing a device with at least one electrophoresis medium chamber and a plurality of electrophoresis channels, wherein each electrophoresis channel of the plurality of electrophoresis channels is an unvented electrophoresis channel. The method also includes providing electrophoresis sieving polymer in the at least one electrophoresis medium chamber; and rotating the device about an axis of rotation while the at least one electrophoresis medium chamber is in fluid communication with each electrophoresis channel of the plurality of electrophoresis channels, wherein the at least one electrophoresis medium chamber is located radially inward from the plurality of electrophoresis channels relative to the axis of rotation. During rotation of the device, the electrophoresis sieving polymer in the at least one electrophoresis medium chamber moves into the plurality of electrophoresis channels.
In another aspect, the present invention provides a device for processing sample material, the device including a substrate with first and second major surfaces and a hub defining an axis of rotation for the substrate; a plurality of electrophoresis channels in the device, wherein the plurality of electrophoresis channels extend generally radially outward relative to the axis of rotation; a plurality of process chambers in the device, each of the process chambers defining a volume for containing sample material. The device further includes a connection structure located between at least one electrophoresis channel of the plurality of electrophoresis channels and at least one process chamber of the plurality of process chambers, wherein the connection structure has a closed configuration in which sample material is prevented from moving into the at least one electrophoresis channel from the at least one process chamber, and wherein the connection structure has an open configuration in which sample material is capable of moving into the at least one electrophoresis channel from the at least one process chamber. Also included in the device is at least one electrophoresis medium chamber in fluid communication with each electrophoresis channel of the plurality of electrophoresis channels.
These and other features and advantages of the invention may be described in connection with various illustrative embodiments of the invention below.